phyluce_assembly_get_fastas_from_match_counts

[mlovelynn]

Hi, I have read through some previous questions on this phyluce function. I tried to troubleshoot by changing the conf file from .conf to .conf.txt. I have copied the exact title of the UCES from the probes.match.sqlite file to the 'all' section in my conf file. I have used this same pipeline without issue on 10 other taxa and now with my new data set I get this error:
File "/Users/corvus/opt/miniconda3/envs/phyluce-1.7.1-x86/bin/phyluce_assembly_get_fastas_from_match_counts", line 306, in
main()
File "/Users/corvus/opt/miniconda3/envs/phyluce-1.7.1-x86/bin/phyluce_assembly_get_fastas_from_match_counts", line 209, in main
len(organisms), os.path.basename(args.match_count_output)
TypeError: object of type 'NoneType' has no len()
I am not sure what else to do to fix this problem. I re-ran the whole pipeline and I use phyluce_assembly_get_fastas_from_match_counts two times before the problem arises after finding invariant loci via HaplotypeCaller. I have attached my pipeline and all files associated with the issue. (I have tried headers 'all' and 'organisms' neither work).
This is the command I am using
phyluce_assembly_get_fastas_from_match_counts
--contigs leptotila-cassinii-refseq-fasta/leptotila-cassinii-refseq-fasta
--locus-db ../leptotila-cassinii-assembled-refseq/leptotila-cassinii-refseq-fasta/uce-search-results/probe.matches.sqlite
--match-count-output leptotila-cassinii-reference-complete-matrix-GQ10-variable-loci.txt
--output leptotila-cassinii-reference.conf \

https://drive.google.com/drive/folders/1W_UQsEP_yR8hxmtEU3Ew2FdcqmInzIiY?usp=drive_link

[brantfaircloth]

I think the biggest error was that the config file was not formatted correct (see attached). Additionally, the parameters used for phyluce_assembly_get_fastas_from_match_counts were also not entirely correct. I placed leptotila-cassinii-refseq.fasta in contigs as in contigs/leptotila-cassinii-refseq.fasta and then I ran:

phyluce_assembly_get_fastas_from_match_counts \
--contigs contigs \
--locus-db probe.matches.sqlite \
--match-count-output leptotila-cassinii-reference-complete-matrix-GQ10-variable-loci.conf \
--output test-leptotila.fasta

and that seemed to work fine. Config file and resulting output are attached. I had to manually add the .txt to each file so Github would allow their upload.

leptotila-cassinii-reference-complete-matrix-GQ10-variable-loci.conf.txt
test-leptotila.fasta.txt